OK. I set LISTIN=POUT. There is a difference in how this restraint:
# 49 VAL HA 52 LYS H 4.11 (#peak 13 #SUP 1.00 #QF 0.99)
&rst
ixpk= 13, nxpk= 0, iat= 810, 868, r1= 1.30, r2= 1.80, r3= 4.11, r4= 4.61,
rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
&end
is read by the Amber10 sander.MPI binary compiled with bugfixes through #17:
******
HA ( 810)-H ( 868) NSTEP1= 0 NSTEP2= 0
R1 = 1.300 R2 = 1.800 R3 = 4.110 R4 = 4.610 RK2 = 20.000 RK3 = 20.000
Rcurr: 3.129 Rcurr-(R2+R3)/2: 0.174 MIN(Rcurr-R2,Rcurr-R3): 0.000
******
and how it's read by the Amber10 sander.MPI binary compiled with bugfixes through #35:
******
HA ( 810)-H ( 868) NSTEP1= 0 NSTEP2= 0
R1 = 4.610 R2 = 4.610 R3 = 4.610 R4 = 4.610 RK2 = 20.000 RK3 = 20.000
Rcurr: 3.129 Rcurr-(R2+R3)/2: 1.481 MIN(Rcurr-R2,Rcurr-R3): 1.481
******
In the second example, R1, R2, R3 and R4 are all set to the same number (= R4 of the input restraint).
Doug
On May 21, 2010, at 3:01 PM, case wrote:
> On Fri, May 21, 2010, Douglas Kojetin wrote:
>
>> Setting pencut = -1.0, here are the first few distance restraints:
>>
>> ---------------------------------------------------------------------------
>> ---
>> First atom Last atom curr. value target deviation penalty
>> ---------------------------------------------------------------------------
>> ---
>> HA VAL 49 -- H LYS 52: 3.143 4.610 1.467 0.000 d
>> 13: 0
>
> OK...now we have progress; you can examine the input data in the RST file,
> looking just at the first restraint. If the solution is not obvious, you
> could post just that one piece of input and ask questions. Also, check
> your mdin file to make sure you have not set some restraint weight to
> zero.
>
> Not to beat a dead horse, but my previous suggestion of setting LISTIN=POUT
> still seems like a good idea -- it gives lots more detail about what is going
> on.
>
> I think it is rather unlikely that this is related to serial vs. parallel, or
> would be fixed by some recompilation. There are lots of ways that restraints
> can do things you don't expect, but difficult to remotely debug without more
> information. (We would need to know r1,r2,r3,r4, rk2, rk3 at a minimum.)
>
> ....dac
>
>
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Received on Sat May 22 2010 - 10:30:04 PDT
